Single-point Energy Calculations Research Articles

Solvent effect on ternary complexes formed by epoxy and hydrofluoric acid

The solvent effect on derivatives of the C2H4O∙∙∙HF∙∙∙HF ternary complex was investigated through the PCM approach and AGOA calculations at the B3LYP/6-311++G(d,p) level of theory. The continuous analysis was useful to verify the profiles of the hydrogen bond distances in the complex, specifically the O∙∙∙H, F∙∙∙H, and F∙∙∙Hβ contacts. On the viewpoint of AGOA, the configurations of the water molecules followed by the measurement of the discrete hydration energies were unveiled.Through the single point energy calculation, the hydration energies were determined through the supermolecule approach, whose values were corrected by the counterpoise correction of the Basis Sets Superposition Error (BSSE). In line with this, the analysis of the Molecular Electrostatic Potential (MEP) revealed positive and negative regions, which represent the interaction sites for the water molecules regarding the oxygen and hydrogen, respectively. In an overview, the acid-catalyzed epoxy ring-opening reaction has distinct interpretations either in vacuum or in aqueous medium whether the most appropriate structure of the C2H4O∙∙∙HF∙∙∙HF trimolecular complex is taken into account.

Calculation of acidity/basicity values of some fluorinated compounds in gas phase and aqueous solution: A computational approach

In this work, acidity/basicity values calculations of some fluorine compounds in gas and aqueous phases were theoretically performed. The gas phase acidity/basicity values were calculated using various computational series including M05-2X, M06-2X and PBE1PBE functionals combined with 6-31+G(d) and 6-31++G(d,p) and 6-311+G(d,p) basis sets. In addition, single point energy calculations in gas phase were carried out at MP2/6-311++G(3df,3pd), M05-2X/aug-cc-pVTZ and M06-2X/aug-cc-pVTZ levels of theory. Beside, CBS-QB3 method was applied to compare with the obtained acidity/basicity values. Results showed that PBE1PBE functional was better than M05-2X and M06-2X functionals. Also, PBE1PBE/aug-cc-PVTZ//PBE1PBE/6-31+G(d), PBE1PBE/aug-cc-PVTZ//PBE1PBE/6-311+G(d,p) and CBS-QB3 series led to MAD equal to 0.9kcalmol−1 and R2>0.9997. As well, the acidity/basicity values of compounds in aqueous phase were computed using obtained solvation free energies with SM8 and CPCM solvation models successfully. Three reliable series containing PBE1PBE/aug-cc-PVTZ//PBE1PBE/6-31+G(d), PBE1PBE/aug-cc-PVTZ//PBE1PBE/6-311+G(d,p) and CBS-QB3 series led to MAD equal to 1.0, 1.0 and 0.8 pKa unit, respectively. Moreover, gas phase acidity/basicity and pKa values of some fluorinated compounds were predicted using purposed reliable methods.

Hydrogen Abstraction Reaction of Hydroxyl Radical with 1,1-Dibromoethane and 1,2-Dibromoethane Studied by Using Semi-Classical Transition State Theory

The hydrogen abstraction reaction by OH radical from CH2BrCH2Br (R1) and CH₃CHBr2 (R2) is investigated theoretically by semi-classical transition state theory. The stationary points for both reactions are located by using ωB97X-D and KMLYP density functional methods along with cc-pVTZ basis. Single-point energy calculations are performed at the QCISD(T) and CCSD(T) levels of theory with different basis sets. The results show that the activation energies are very sensitive to effects of electron correlation and basis set. In order to correct basis set effects on the calculated energetic, a correction factor (CF) is determined from the energy difference between the MP2/cc-pVTZ and MP2/aug-cc-pVTZ levels. xij vibrational anharmonicity coefficients, needed for semi-classical transition state theory, are calculated at the KMLYP/cc-pVTZ level of theory. Thermal rate coefficients are computed over the temperature range from 200 to 3000 K and they are shown to be in accordance with available experimental data. The computed rate constants for the reactions R1 and R2 are fitted to the equation k(T)=A T^n exp[-E(T+T_0 )/(T^2+ T_0^2 ) ].

A disparate 3-D silver(I) coordination polymer of pyridine-3,5-dicarboxylate and pyrimidine with strong intermetallic interactions: X-ray crystallography, photoluminescence and antimicrobial activity

A polymeric silver(I) complex, [Ag4(μ-pydc)2(μ-pm)2]n (1) (pydc = pyridine-3,5-dicarboxylate and pm = pyrimidine), has been synthesized and characterized by elemental analysis, IR spectroscopy, thermal analysis, and single-crystal X-ray diffraction. X-ray crystallographic data of 1 revealed that pydc exhibits two different coordinaton modes that play a key role in the construction of the 3-D crystal network including Ag–carboxylate clusters in which close Ag–Ag distances exist. The magnitudes of close Ag–Ag interactions in second-order energy (E2) have been revealed by natural bond orbital analysis performed with single point energy calculation using the experimental geometry of 1. Furthermore, the luminescent properties of 1 show strong fluorescence with two emission maxima in the visible region. Also, 1 has antifungal activity on Candida albicans (MIC value, 4 μg mL−1) and good antibacterial activity on micro-organisms (MIC value, 64–256 μg mL−1).

A computational study on kinetics, mechanism and thermochemistry of gas-phase reactions of 3-hydroxy-2-butanone with OH radicals

Theoretical investigation has been carried out on the kinetics and reaction mechanism of the gas-phase reaction of 3-hydroxy-2-butanone (3H2B) with OH radical using dual-level procedure employing the optimization at DFT(BHandHLYP)/6-311 ++G(d,p) followed by a single-point energy calculation at the CCSD(T)/6-311 ++G(d,p) level of theory. The pre- and post reactive complexes are also validated at entrance and exit channels, respectively. Thus reaction may be proceed via indirect mechanism. The intrinsic reaction coordinate (IRC) calculation has also been performed to confirm the smooth transition from a reactant to product through the respective transition states. The rate coefficients were calculated for the first time over a wide range of temperature (250–450 K) and described by the following expression: kOH = 7.56 × 10−11exp[ −(549.3 ± 11.2)/T] cm3 molecule−1s−1. At 298 K, our calculated rate coefficient 1.20 × 10−11 cm3 molecule−1 s−1 is in good agreement with the experimental results. Our calculation indicates that H-abstraction from α-C-H site of 3H2B is the dominant reaction channel. Using group-balanced isodesmic reactions, the standard enthalpies of formation for 3H2B and radicals generated by hydrogen abstraction are reported for the first time. The branching ratios of the different reaction channels are also determined. Also, the atmospheric lifetime of 3H2B is also calculated to be 1.04 days. Gas-phase reactions of 3-hydroxy-2-butanone with OH radicals at 298 K were studied.

Theoretical study on the properties and stabilities of complexes formed between SO4(C2v) and isostructure species of CO2, CS2, and SCO.

In this work ab initio calculations at MP2 level in conjugation with aug-cc-pVXZ (X=D and T) basis set were performed in order to examine complexes formed between SO4 and each of linear molecules of CO2, CS2, and SCO. The results have been discussed on real minima located on singlet potential energy surface (PES). Single-point energy calculations at the MP2/aug-cc-pVTZ level uphold results obtained at the MP2/aug-cc-pVDZ level. The atom in molecules theory (AIM) was utilized to analyze the nature of intermolecular interactions. Also, natural bond orbital (NBO) analysis has been used in order to get charge transfer quota in complexes. The results show that the atmospheric role of SO4-CS2 system is more important than those followed by SO4-SCO and SO4-CO2, respectively.

Theoretical Kinetics Studies on the Reaction of CF3CF═CF2 with Hydroxyl Radical

The potential energy surface for the reaction of hexafluoropropene with hydroxyl radical is explored by using BB1K density functional method. Single-point energy calculations are performed at CBS-Q level of theory. Semiclassical transition state theory and a modified strong collision/RRKM model are employed to calculate the thermal rate coefficients for the formation of major products as a function of temperature and pressure. It is revealed from the computed rate constants that the major product channels at low temperatures and high pressures are the formation of the primary adducts formed through OH addition to the double bond of CF3═CFCF2. At high temperatures and low pressures, however, many products arising from unimolecular decomposition of the chemically activated intermediates become important. P9A (CF3CFCOF + HF) and P7B (CF3COCF2 + HF) are dominant products at elevated temperatures. Semiclassical transition state theory is used to compute the overall high-pressure rate constants over the temperature range of 200-1500 K. The computed rate constants are in accordance with the available experimental data.

Computational approaches for efficiently modelling of small atmospheric clusters

Utilizing a comprehensive test set of 205 clusters of atmospheric relevance, we investigate how different DFT functionals (M06-2X, PW91, ωB97X-D) and basis sets (6-311++G(3df,3pd), 6-31++G(d,p), 6-31+G(d)) affect the thermal contribution to the Gibbs free energy and single point energy. Reducing the basis set used in the geometry and frequency calculation from 6-311++G(3df,3pd)→6-31++G(d,p) implies a significant speed-up in computational time and only leads to small errors in the thermal contribution to the Gibbs free energy and subsequent coupled cluster single point energy calculation.

Theoretical investigation on mechanism and kinetics of the Cl-initiated hydrogen abstraction reactions of ethyl trifluoroacetate at 298 K.

Theoretical investigations were carried out on the gas-phase reactions of CF3C(O)OCH2CH3, ethyl trifluoroacetate (ETFA) with Cl atoms by means of modern density functional theory methods. The optimized geometries, frequencies and minimum energy path were obtained with the hybrid density functional model MPWB1K using the 6-31+G(d,p) basis set. The single point energy calculations were refined further using the G2(MP2) method. Two conformers relatively close in energy were identified for ETFA; both are likely to be important in the temperature range of our study. The existence of transition states on the corresponding potential energy surface was ascertained by performing intrinsic reaction coordinate calculations. The rate constant at 298 K calculated theoretically using canonical transition state theory was found to be in good agreement with experimentally measured values. Our calculations suggest that H abstraction from the -CH2 group is kinetically and thermodynamically more favorable than abstraction from the -CH3 group. The atmospheric lifetime of ETFA with Cl atoms was determined to be 1.98 years. To the best of our knowledge, this work represents the first determination of the rate coefficients for the gas-phase reaction of chlorine atoms in ETFA.

Reactivity of CHI3 with OH radicals: X-abstraction reaction pathways (X = H, I), atmospheric chemistry, and nuclear safety.

The X-abstraction (X = H, I) pathways in the reaction of CHI3 with OH radical, a possible iodoform removal process relevant to the Earth's atmosphere and conditions prevailing in the case of a nuclear accident, have been studied applying highly correlated ab initio quantum chemistry methods and canonical transition-state theory to obtain reaction energy profiles and rate constants. Geometry optimizations of reactants, products, molecular complexes, and transition states determined at the MP2/cc-pVTZ level of theory have been followed by DK-CCSD(T)/ANO-RCC single-point energy calculations. Further improvement of electronic energies has been achieved by applying spin-orbit coupling, corrections toward full configuration interaction, vibration contributions, and tunneling corrections. Calculated reaction enthalpies at 0 K are -108.2 and -5.1 kJ mol(-1) for the H- and I-abstraction pathways, respectively; the strongly exothermic H-abstraction pathway is energetically favored over the modestly exothermic I-abstraction one. The overall rate constant at 298 K based on our ab initio calculations is 4.90 × 10(-11) cm(3) molecule(-1) s(-1), with the I-abstraction pathway being the major channel over the temperature range of 250-2000 K. The CHI3 atmospheric lifetime with respect to the removal reaction with OH radical is predicted to be about 6 h, very short compared to that of other halomethanes.

Gas-phase thermochemical properties of some tri-substituted phenols: A density functional theory study

The study of the energetics of phenolic compounds has a considerable practical interest since this family of compounds includes numerous synthetic and naturally occurring antioxidants. In this work, density functional theory (DFT) has been used to investigate gas-phase thermochemical properties of the following tri-substituted phenols: 2,4,6-trimethylphenol, 2,6-dimethyl-4-tert-butylphenol, 2,6-dimethyl-4-methoxyphenol, 2,4,6-tri-tert-butylphenol, 2,6-di-tert-butyl-4-methylphenol, 2,6-di-tert-butyl-4-methoxyphenol, 2,4,6-trimethoxyphenol, 2,6-dimethoxy-4-methylphenol and 2,6-dimethoxy-4-tert-butylphenol. Molecular structures were computed with the B3LYP and the ωB97X-D functionals and the 6-31G(d) basis set. More accurate energies were obtained from single-point energy calculations with both functionals and the 6-311++G(2df,2pd) basis set. Standard enthalpies of formation of the phenolic molecules and phenoxyl radicals were derived using an appropriate homodesmotic reaction. The OH homolytic bond dissociation enthalpies, gas-phase acidities and adiabatic ionization enthalpies were also calculated. The general good agreement found between the calculated and the few existent experimental gas-phase thermochemical parameters gives confidence to the estimates concerning the phenolic compounds which were not yet experimentally studied.

Quantum chemical study on the atmospheric photooxidation of ethyl acetate

The mechanism for OH radical initiated atmospheric photoxidation reaction of ethyl acetate was carried out by using the density functional theory method. Geometries have been optimized at the B3LYP level with a standard 6-31G(d,p) basis set. The single-point energy calculations have been performed at the MP2/6-31G(d), MP2/6-311++G(d,p), and CCSD(T)/6-31G(d) levels, respectively. All of the possible degradation channels involved in the oxidation of ethyl acetate by OH radicals have been presented and discussed. Among the five possible hydrogen abstraction pathways of the reaction of ethyl acetate with OH radicals, the hydrogen abstractions from the C1–H3 and C2–H5 bonds are the dominant reaction pathways due to the low potential barriers and strong exothermicity. The β-ester rearrangement of IM6 is energetically favorable but is not expected to be important. The α-ester rearrangement reaction and O2 direct abstraction from IM17 are the more favorable pathways and are strongly competitive. In addition, the α-ester rearrangement reaction is confirmed to be a one-step process. Acetic acid, formic acetic anhydride, acetoxyacetaldehyde, and acetic anhydride are the main products for the reaction of ethyl acetate with OH radicals.

Theoretical study for OH radical-initiated atmospheric oxidation of ethyl acrylate

OH radical-initiated atmospheric oxidation of ethyl acrylate (ethyl 2-propenoate, EA) has been investigated by performing density functional theory (DFT) calculations. Optimizations of the reactants, intermediates, transition states and products were carried out at the MPWB1K/6-31+G(d,p) level. Single-point energy calculations were performed at the MPWB1K/6-311+G(3df,2p) level of theory. The detailed oxidation mechanism was presented and discussed. The results show that the OH addition is more energetically favorable than the H abstraction. Rice–Ramsperger–Kassel–Marcus (RRKM) theory was used to predict the rate constants over the possible atmospheric temperature range of 180–370K. The Arrhenius expression adequately describes the total rate constant: k(EA+OH)=(1.71×10−12)exp(805.42/T)cm3molecule−1s−1. At 298K, the atmospheric lifetime of ethyl acrylate determined by OH radicals is about 16.2h. In order to find out the effect of alkyl substitution on the reaction activity, rate constants for the reactions of methyl acrylate, methyl methacrylate and butyl acrylate with OH radicals were also discussed. Calculation results show that the reaction activity may increase with the increased electron-donating substitution for electrophilic addition reaction.

Benchmark study on methanol C-H and O-H bond activation by bare [Fe(IV)O](2+).

We present a high-level computational study on methanol C-H and O-H bond cleavages by bare [Fe(IV)O](2+), as well as benchmarks of various density functional theory (DFT) methods. We considered direct and concerted hydrogen transfer (DHT and CHT) pathways, respectively. The potential energy surfaces were constructed at the CCSD(T)/def2-TZVPP//B3LYP/def2-TZVP level of theory. Mechanistically, (1) the C-H bond cleavage is dominant and the O-H activation only plays minor role on the PESs; (2) the DHT from methyl should be the most practical channel; and (3) electronic structure analysis demonstrates the proton and electron transfer coupling behavior along the reaction coordinates. The solvent effect is evident and plays distinct roles in regulating the two bond activations in different mechanisms during the catalysis. The effect of optimizing the geometries using different density functionals was also studied, showing that it is not meaningful to discuss which DFT method could give the accurate prediction of the geometries, especially for transition structures. Furthermore, the gold-standard CCSD(T) method was used to benchmark 19 different density functionals with different Hartree-Fock exchange fractions. The results revealed that (i) the structural factor plays a minor role in the single point energy (SPE) calculations; (ii) reaction energy prediction is quite challenging for DFT methods; (iii) the mean absolute deviations (MADs) reflect the problematic description of the DFs when dealing with metal oxidation state change, giving a strong correlation on the HF exchange in the DFs. Knowledge from this study should be of great value for computational chemistry, especially for the de novo design of transition metal catalysts.

Screening of Potential TM-Olivine Candidates As Cathodes for Mg-Ion Batteries

Alternatives to Li-ion batteries are of increasing interest, mainly due to the ever increasing need for good and reliable rechargeable batteries for energy storage and delivery in a wide variety of applications, while recognizing that Li is a very limited resource. Mg ions are considered promising alternative charge carrier candidates in novel ion batteries due to the high theoretical volumetric capacity of Mg, its high abundance in the earth crust, and its stability for handling and electrode preparation processes despite high potential reactivity. However, replacing Li with Mg in conventional ion batteries is not straight forward, particularly due to the switch from monovalent to divalent ions. Changing the charge carrying ion imposes large changes on the chemical environment, thus providing the scientific community with a huge challenge in finding good anode and cathode materials, as well as electrolytes and container materials that all work together. The present work focuses on olivine-structured materials as potential cathodes, studied by theoretical methods. The work is carried out in close collaboration with experimental studies.Atomic scale calculations of the olivine structure, MgTMSiO4, with varying transition metals (TM), were performed with the Vienna ab initio simulation package (VASP). This is a density functional theory (DFT) code and the PBE generalized gradient approximation (GGA) was chosen. The unit cell was allowed to relax during ionic optimisations, and single point energy calculations on the final structure were performed for the final electronic relaxation. Hybrid calculations with 25% Hartree-Fock exchange were performed as benchmark single point calculations for some structures, as well as Hubbard GGA+U calculations to investigate the effect of localized strongly correlated d electrons.We will present results on a number of TMs in order to screen promising candidates from a thermodynamic and kinetic point of view. Some preliminary results are shown in Figure 1. Figure 1a shows that for MgTMSiO4 with TM = V, Mn and Fe, the formation of an intermediary MgxTMSiO4, x=0.25, 0.5 or 0.75, is stable with respect to the extremes with full or no magnesiation. Unit cell expansion during the uptake and release of Mg may be of crucial importance for long term stability of the final cathode. Figure 1b) shows that the maximum unit cell expansion from TMSiO4 to MgTMSiO4 is much more prominent for TM= Mn than TM = V or Fe.Nudged elastic band (NEB) calculations for the diffusion of Mg between different sites in MgMnSiO4 are shown in Figure 1c and d. Figure 1c shows that moving Mg from to a neighbouring (empty) Mg site has a 1 eV barrier. It should be noted that although the unit cell contains 4 formula units, removing either of the four Mg atoms gives 4 equivalent Mg0.75MnSiO4. This is reflected in Figure 1c where the start and end points of the NEB path are at the same energy level. In the perfect MgMnSiO4 crystal Mg occupies sites denoted 4a, and Mn the sites denoted 4c. However, scrambling is possible, and Figure 1d shows the NEB path for Mg diffusing to an empty Mn (4c) site in the case of MgMn0.75SiO4. The 0.8 eV energy difference between end and start point indicates that empty 4c sites are thermodynamically unfavourable for MgMnSiO4 and that defects arising from Mn vacancies are easily reoccupied by Mg.Figure 1 Preliminary results of calculations on MgTMSiO4 olivine materials as potential candidates for cathodes in Mg-ion batteries. (a) Reaction energies for x MgTMSiO4 + (1-x) TMSiO4 → MgxTMSiO4. (b) Maximum unit cell expansion during magnesiation. NEB-path with diffusion energies when Mg diffuses from (c) one 4a to a neighbouring 4a position in Mg0.75MnSiO4 (d) from a 4a to a 4c site in MgMn0.75SiO4.

Structural and Electronic Properties of Carbon-Nanotube/Graphene Junction: A First-Principles Study

Recently, a junction made of single wall carbon nanotube and a single sheet of graphene has been fabricated on silicon oxide substrate [1]. Their Raman spectroscopy measurements showed an upshift of the radial breathing modes and G peaks of the nanotube attributed to the charge transfer (CT) at the junction. The direction of the CT was determined from the intensity ratio of 2D/G of graphene, decreasing as a function of G Raman shift, which suggest n-doping of graphene due to the presence of nanotube. Their theoretical work, using molecular dynamics simulation, ruled out the strain on carbon nanotube to be the cause of the Raman upshift. In this work, we perform density functional theory calculations, for a model of C(13,7)/graphene junction, as suggested in Ref. [1]. Figure-1 shows the adopted model with 1132 carbon atoms, rendering the conventional first-principles methods that scale as O(N3) impractical. Therefore, we carried out the optimization of the large model using self-consistent density functional tight-binding method (SCC-DFTB), provided within CP2K package [2]. The resulting structure was then used to perform a single point energy calculation within density functional theory (DFT), adopting B97-D functional [3, 4], suitable for non-covalent interactions. The DFT is based on QUICKSTEP [5], which is an order-N method implemented in CP2K. Our preliminary results indicate that the charge transfer for a suspended nanotube/graphene system takes place from graphene to the carbon nanotube. To ascertain these results, we built a small material model consisting of the armchair C(10,10) and graphene junction, and performed calculations with the VASP package using optPBE [6] functional, which also includes the dispersion to account for van der Waals interactions. The results for the small model suggest an n-doping of carbon nanotube. Our findings are in agreement with the work of Cook et al. [7] for a C(8,0) adsorbed on a flat graphene junction. As can be seen, all the theoretical work seem to be in disagreement with the charge transfer direction, suggested in Ref. [1], which may be due to the pristine nature of the models. In this paper we will report on structural and electronic properties of a CNT/graphene junction, for pristine models as well as doped systems with impurities, where charge re-distribution at the junction will be outlined.1. Geraldine L. C. Paulus, et al., Charge Transfer at Junctions of a Single Layer of Graphene and a Metallic Single Walled Carbon Nanotube. Small, 2013. 9: p. 1954.2. CP2K. Available from: http://www.cp2k.org.3. Grimme, S., Semiemperical GGA-type density functional constructed with long-range dispersion correction. J. Comput. Chem., 2006. 27: p. 1787.4. Becke, A.D., Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J. Chem. Phys., 1997. 107: p. 8554.5. J. VandeVondele, et al., QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. J. Comput. Phys. Commun., 2005. 167: p. 103.6. Klimes, J., D.R. Bowler, and A. Michaelides, Van der Waals density functionals applied to solids. Phys. Rev. B, 2011. 83: p. 195131.7. Brandon G. Cook, William R. French, and a.K. Varga, Electron Transport properties of carbon nanotube-graphene contacts. Appl. Phys. Lett., 2012. 101: p. 153501.

Effect of Single Wall Carbon Nanotubes on the Conformation of Poly(vinylidene fluoride)

Structures consisting of single Poly(vinylidene fluoride) (PVDF) chains, single wall carbon nanotubes (SWCNTs), a PVDF chain interacting with a SWCNT and of five PVDF chains arranged to resemble the α and β crystal structures of PVDF were evaluated using geometry optimizations and single point energy calculations. Density functional theory with dispersion correction was used for all calculations. The conformer of PVDF is the lowest energy structure, irrespective of whether the SWCNT is present or not. Interaction with the SWCNT reduces the energy difference between the β and α conformers by approximately 30%, indicating that SWCNTs can increase the relative amount of the β conformers at higher temperatures. However, even in the presence of the SWCNT this energy difference is approximately 1.67 kcal/mol per –CH2CF2– repeat unit, which is larger than kT at 300 K (0.6 kcal/mol). Hence, the presence of the SWCNTs is not expected to substantially increase the relative amount of the β conformers at these conditions. Compression of the α and β crystal structures, which occurs during fibre extrusion, and which may be increased if nanoparticles are present in the polymer matrix, further decreases the energy difference between the β and α conformers but only to a very small extent at pressures relevant to fibre extrusion.

Intrinsic affinities of alkali metal cations for diaza-18-crown-6: Effects of alkali metal cation size and donor atoms on the binding energies

Threshold collision-induced dissociation of alkali metal cation-diaza-18-crown-6 complexes, M+(da18C6), with xenon is studied using guided ion beam tandem mass spectrometry techniques. The alkali metal cations examined here include: Na+, K+, Rb+, and Cs+. In all cases, M+ is the only product observed, corresponding to endothermic loss of the intact da18C6 ligand. The cross section thresholds are analyzed to extract zero and 298K M+da18C6 bond dissociation energies (BDEs) after properly accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and the lifetimes for dissociation. Density functional theory calculations at the B3LYP/def2-TZVPPD and B3LYP/6-31+G* levels of theory are used to determine the structures of da18C6 and the M+(da18C6) complexes and provide molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical BDEs are determined from single point energy calculations at the B3LYP and MP2(full) levels of theory using the def2-TZVPPD and 6-311+G(2d,2p) basis sets using the B3LYP/def2-TZVPPD and B3LYP/6-31+G* optimized geometries. The agreement between B3LYP/def2-TZVPPD theory and experiment is excellent for all four M+(da18C6) complexes. The M+da18C6 BDEs decrease as the size of the alkali metal cation increases, consistent with the electrostatic nature of the binding in these complexes. The M+(da18C6) structures and BDEs are compared to those previously reported for the analogous complexes of 18-crown-6 and hexaaza-18-crown-6, to examine the effects of the donor atoms (N versus O) on the structure and strength of binding.

Infrared multiple photon dissociation action spectroscopy of sodium cationized halouracils: Effects of sodium cationization and halogenation on gas-phase conformation

The gas-phase structures of sodium cationized complexes of 5- and 6-halo-substituted uracils are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The halouracils examined in this investigation include: 5-flourouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, and 6-chlorouracil. Experimental IRMPD action spectra of the sodium cationized halouracil complexes are measured using a 4.7T Fourier transform ion cyclotron resonance mass spectrometer coupled to the FELIX free electron laser (FEL). Irradiation of the mass selected sodium cationized halouracil complexes by the FEL was carried out over the range of frequencies extending from 950 to 1900cm−1. Theoretical linear IR spectra predicted for the stable low-energy conformations of the sodium cationized halouracils, calculated at B3LYP/6-31G(d) level of theory, are compared with the measured IRMPD action spectra to identify the structures accessed in the experiments. Relative stabilities of the low-energy conformations are determined from single-point energy calculations performed at the B3LYP/6-311+G(2d,2p) level of theory. The evolution of IRMPD spectral features as a function of the size (F, Cl, Br, and I) and position (5 versus 6) of the halogen substituent are examined to elucidate the effects of the halogen substituent and noncovalent interactions with sodium cations on the structure of the nucleobase. Present results are compared with results from energy-resolved collision-induced dissociation and IRMPD action spectroscopy studies previously reported for the protonated and sodium cationized forms of uracil, and halo-, methyl-, and thioketo-substituted uracils. The present results suggest that only a single conformer is accessed for all of the 5-halouracil complexes, whereas multiple conformers are accessed for the Na+(6ClU) complex. In all cases, the experimental IRMPD action spectra confirm that the sodium cation binds to the O4 carbonyl oxygen atom of the canonical diketo tautomer in the ground-state conformers, and gains additional stabilization via chelation interactions with the halogen substituent in the complexes to the 5-halouracils as predicted by theory.

Kinetics and mechanism for chlorine-initiated atmospheric oxidation of ethyl formate

The chlorine-initiated reaction mechanism of ethyl formate in the atmosphere was investigated using the density functional theory method. The geometry parameters and frequencies of all of the stationary points were calculated at the B3LYP/ 6-31G(d,p) level. The single-point energy calculations were carried out at different levels, including MP2/6-31G(d), MP2/6-311++G(d,p), and CCSD(T)/6-31G(d). A detailed oxidation mechanism is provided and discussed. Present results show that α-ester rearrangement reaction and the O2 direct abstraction from IM6 (HC(O)OCH(O)CH3) are the more favorable pathway and are competitive. The 1,4-H shift isomerization of IM6 proved to be feasible under general atmospheric conditions. The decomposition of IM18 (CH3CH2OC(O)O) is favorable both thermodynamically and kinetically. Canonical variational transition theory with small-curvature tunneling correction was employed to predict the rate constants. The overall rate constant of ethyl formate at 298 K is 8.63 × 10−12 cm3 molecule−1 s−1. The Arrhenius equations of rate constants at the temperature range of 200–380 K were fitted.